Doctor Whooves Episode 1: The Doctor in the Box
by The 1597 Faceless Writer
Summary: The Doctor suddenly finds himself in the magical land of Equestria and soon discovers that he's regenerated into a pony. As Twilight Sparkle tries to learn more about the Doctor with the help of Spike and Princess Luna, a creature from the Doctor's past arrives in Ponyville with evil intentions.
1. Prologue

Author's Note: I've been a fan of MLP: FiM for a while now and I've recently gotten into Doctor Who. I decided to make my own series of Doctor Who/MLP: FiM crossover stories. Each story will be like an episode in a TV series and will consist of a few chapters each. Normally I'll upload at least one episode each week, unless I'm taking a hiatus or am busy with another story. I hope all of you Doctor Who and MLP: FiM fans enjoy this. Lastly, I'd like to note that I do not own any unoriginal characters in these "episodes" and all rights go to the respective television companies.

Doctor Whooves: Episode 1

The Doctor in the Box

Prologue

_**Canterlot Castle, Canterlot, Equestria, Gaia, Spring, 1000 C.E.**_

The night was cool and the sky was glistening with an infinite number of stars. The brightest light in the sky, obviously, was the Moon. It's radiant, eerie light covered the land below in a mystical blanket of secrets and magic. Princess Celestia sat calmly by the window sill. She stared up at the Moon with great concentration. She looked at the celestial body as if there was something...or somepony looking back at her. Only she knew this fact to be true. There, indeed, was somepony up there. It had been difficult to keep the truth from the rest of Equestria. It pained her to keep the secret buried within her but it was unavoidable. If the citizens of Equestria, and the world for that matter, found out that the Tale of the Regal Sisters was true, then all hell would break loose. Then again, it was only a matter of time before _she_ returned to Equestria. She would have to face _her_ once again. But, by this point, even Celestia herself was foggy on the subject of the return of her sister. She turned away from the Moon and looked back at it again.

"I...I'm sorry, Luna," Celestia breathed. "If only things had worked out differently."

She held back the ancient tears inside her and turned away from the glowing orb. She walked further into her room and fell upon the bed. She looked around the room and, once again, examined the seemingly endless rows of pictures of her _predecessors_. Other ponies looked at them and saw the countless ancestors of Princess Celestia. All Princess Celestia saw was herself. Many different looks and names. Too many to count and remember immediately. Luckily there was a library to keep track so she didn't have to worry about forgetting her past "lives".

She turned towards the calender and looked at the date. It was now only a few weeks until the 1000th Summer Sun Celebration. 1000 years since her solo reign began. 1000 years since Luna was banished. She tried to block the thought from her head but, no matter what she tried, she couldn't forget that day. That moment. The moment that Luna was sent away to the Moon to live out the rest of her never-ending life.

Celestia shook her head and tried to think of other things. Like her faithful student, Twilight Sparkle. A sharp pony indeed. Definitely had a bright and fantastic future ahead of her...if only she'd come out of that library every once in awhile and try to make some friends. Well, at least she had Spike so that was better than nothing. But still, there had to be something she could do for that antisocial unicorn. Then her mind drifted back to the Moon. To the face of her sister. Her lovely sister. Her powerful sister. Her vengeful sister.

She turned her thoughts away from the Moon again and went back to her plans for the Summer Sun Celebration.

"Hmm...so I've got to choose a town for the celebration again," she said out loud. "Manehattan's too busy. Fillydelphia looks like an option, though."

Suddenly, the room was filled with a strange, foreign sound that Celestia had never heard before. Or had she? It sounded so familiar. She must had heard something like it before. It was a sound too wondrous and weird to explain in words. She watched in amazement as a strange blue box appeared in the middle of her room.

The box was made of wood, had windows on its sides, and had the words _Police Public Call Box_ printed on the top. Celestia climbed off her bed and slowly approached the box. She had definitely seen this box somewhere before. Somewhere in her past. Somewhere in her clouded, long, confusing past.

The door to the box flung open and Celestia stepped back. Through the door appeared a male earth pony with a chestnut coat, dark brown mane, an hourglass cutie mark, a dark blue suit, and a red tie.

"I wonder if I've finally made it back to the right time," said the stallion. The stallion saw Celestia and their eyes met in an awkward stare. "Ah! Princess! So nice to see you!" The stallion emerged completely from the box and approached the Princess. He casually shook her hoof and walked over towards the window. "Nice night, isn't it?"

"I...I think I know you from somewhere," said Celestia.

"Why of course you know me! We've seen each other enough times!"

"I'm sorry but...I don't think I truly know you."

The stallion turned around and faced the Princess. He walked towards her until he was only a few feet from where she was standing.

"Tell me, Princess Celestia. What is the time?" he asked.

"Well it's almost nine o'clock," she replied.

"No, no, no! I mean the year! Time of year! That sort of thing."

"It's the spring of 1000 if that's what you're asking."

"Spring of 1000. Damn! I'm a few years off! Oh...sorry for the intrusion, Princess. I shall be out of your hair...er...mane in a flash!"

The stallion began walking towards the box but the Princess stopped him.

"Wait!" she stated. The stallion turned around to face her once again. "Who are you?"

"I'm the Doctor," replied the stallion. "You'll come to know me very well quite soon."

"I think I've seen you somewhere before."

"Well you have. Many times in fact. We just won't be properly introduced for another couple years."

"What are you? A time traveler?"

"Pretty much, though I do have more under my belt than just traveling through time."

"Amazing. I've never met a time traveling pony before!"

"Well technically you have since we have met before."

"Oh...yes...that's true."

"Well, I apologize Princess but I must be off. Places to go, people and ponies to see!"

The Doctor broke free from the Princess's grasp and walked towards the box. Just before entering it he turned around to face the Princess one final time.

"By the way," he said. Celestia was all ears. "Spring of 1000 is what you said?"

"Yes," she replied.

"Spring of 1000. Ah! You have a very special Summer Sun Celebration on the way! Might I suggest you have it take place in Ponyville this year."

"Ponyville?"

"Yes! Oh and make sure that Twilight Sparkle is involved in it."

"Twilight Sparkle? My student?"

"Yes! Trust me. She's going to help out a lot and this is going to be one Summer Sun Celebration to remember! Goodbye, Princess Celestia!"

"Goodbye...Doctor."

The Doctor then turned away from the Princess and yelled, "Allons-y!", as he went through the doorway leading into the box. The Princess watched as the box began emitting the strange sound again. The light on the top of the box flickered as the box slowly vanished into thin air. The Princess walked back towards her bed and stood next to it, dazed by what had just happened.

"Hmm...Ponyville," she breathed. "Sounds promising."

She then started rummaging through some old town files as the Moon slowly vanished behind a wall of clouds.


	2. House Call

Author's Note: I'd just like to state that this series starts off after the season 2 finale of MLP: FiM, A Canterlot Wedding Part 2 (which in this timeline took place in the spring of 1002 C.E.) and immediately after the ending of the Doctor Who season 4 finale, The End of Time Part 2. That's all I have to say.

Chapter 1: House Call

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Twilight Sparkle gave a long sigh as she fell to the floor, exhausted from the tiring events of that day. She had been working all day to help the citizens of Ponyville prepare themselves for the upcoming Summer Sun Celebration. Some of the other ponies in town found it strange that Princess Celestia was having the celebration in Ponyville with it being only a mere two years since the last time it was held in Ponyville. Twilight was also confused, just like the others, but she was happy nonetheless. The past few days had been extremely busy with arrangements, meetings, and making sure that everypony was doing their job correctly. It was now only three days until the Summer Sun Celebration and anxiety had spread among the ponies of Ponyville like the plague. At least the town was organized and prepared due to the plans directed by Twilight herself. Everypony was still busy getting all of the preparations together but Twilight had no more strength to work at the current moment.

"Twilight! Twilight!" called the anxious voice of Spike the dragon. Twilight crawled over to the couch and sprawled herself on top of it.

"Yes, Spike?" she asked weakly as her muscles slowly began to relax. The small purple and green dragon ran down the stairs and approached the couch, a note flapping wildly in his claw.

"You got this note this morning but you left before I could give it to you."

"Sorry. I had a lot to do today. Who's it from?"

"Princess Luna."

"Can you read it to me, please? It's been a really long day."

Spike rolled his eyes and examined the letter. There wasn't much on it.

"Dear Twilight Sparkle," he read. "I have received your notice and shall be visiting your residence at the time you requested. We can discuss things further then. Hoping you are well, Princess Luna."

Twilight's head jerked up and she used her magic to levitate the letter over to her.

"Princess Luna is coming?" she asked with a stunned look.

"I thought you were too tired to read it!" Spike snapped with a sarcastic grin.

"Nevermind that, Spike! Princess Luna is coming...and this place is a disaster!"

She hopped off of the couch and looked around the library. Books, papers, and many other miscellaneous objects were scattered all over the place.

"If this place is a disaster then _why_ did you ask her to come, anyway?" asked Spike.

"I didn't! Let's see. I have received your notice and shall be visiting your residence at the time you requested? I never sent Princess Luna a notice!"

"Are you sure?"

"I'm positive, Spike! I've been too busy these past few days to write a letter to anypony!"

"Maybe you did it in your sleep!"

"You would have had to help me send it. Unless you're saying that you slept walked too."

"Hmm. Maybe somepony's cast a dark curse on us! What if Trixie's come back for revenge?"

"Please. If somepony did cast a curse on us I'd highly doubt that it would be Trixie. This is suspicious, though. I guess I'll figure out the details of this supposed letter from me when the Princess arrives."

Twilight turned towards the nearby clock and saw that it was now 5:30 in the evening. Just then, there were three loud knocks on the door.

"That's probably her," said Spike. Twilight gulped and approached the door. She opened it and was greeted with the sight of the majestically blue Princess Luna.

"Good evening, Twilight Sparkle," she said. Twilight and Spike bowed politely as she walked through the door. "My, my. You've certainly got an...interesting way of organizing your belongings."

"I apologize, Princess. The other ponies and I have been busy preparing for the 1002nd Summer Sun Celebration," said Twilight.

"Please call me Luna and I completely understand. Manehattan was disastrous last year."

"Isn't that place always disastrous?" Spike asked. Luna chuckled and walked towards a nearby cushion to sit down. Twilight and Spike followed her and sat down on the couch.

"So. What is it that you wanted to speak with me about?" she asked. Twilight and Spike turned to each other nervously and then turned back towards Luna.

"Pri...Luna, I know this is going to sound weird but I couldn't have been the one who sent you this supposed notice you mentioned in your letter," breathed the lavender unicorn.

"What do you mean?"

"I mean I haven't sent any letters to you. Heck, I haven't sent any letters period. I've been too busy."

"Then how to you explain this?"

Luna's horn shone for a few seconds before another piece of paper appeared out of thin air. It floated over to Twilight and she read it.

"Dear Princess Luna," Twilight read. "I would like you to come and visit me at half past five in the evening three days prior to the upcoming Summer Sun Celebration. Do whatever you can but please come. I really need to discuss something with you and...there's something I need to show you. I'll explain everything when you get here. Hoping you and Princess Celestia are well, Twilight Sparkle."

Twilight scanned the letter several times. It was unmistakable. This was her own writing! But it couldn't be. Or could it? Twilight suddenly remembered the time she went back in time to prevent herself from worrying, only to cause her past self to start worrying in the first place.

"See?" stated Luna. "You sent me a letter."

"But...I couldn't have, and yet here it is. This is definitely my hornwriting!"

Luna stared at Twilight for a few seconds and then began to laugh.

"Ha ha! Are you playing a trick on me, Twilight?" she laughed. "It isn't even Nightmare Night and you're already pulling pranks on me! I can see why my sister has a strong liking of you!"

"I'm sorry, Luna, but I'm not joking. This letter was definitely written by me but I didn't write it!"

The smile faded from Luna's face and she cocked her head slightly.

"Come now. Are you saying that you haven't written a note that you've written? That statement alone is an obvious contradiction!"

"I told you, Twilight! It's a curse!" Spike panicked. Twilight shoved the dragon slightly and stood up.

"I'm telling you the truth, Luna. I haven't written or sent any note to you," said Twilight. Luna sighed and Spike scratched his head with confusion. "Luna, when did you get this note?"

"I got it this morning but the guards said that it arrived last night," Luna replied.

"How? How did it get there?"

"They didn't really know. It just seemed to appear in the mail room. Nothing came in or out of that room. However, they did state that they heard an awfully strange noise from inside the room, but when they checked they found nothing."

"Strange. Hmm...what if...this is a letter that I'm _going_ to write?"

"Are you suggesting that this could be a letter from the future?"

"Time travel's possible. Though it's very complicated and hard to control. Trust me...I've done it before."

"Well if this is from the future...then I guess I'm needed here at this specific time for a specific purpose."

"But what could it be?" Spike asked.

"I'm not sure. But I've got a feeling that we're going to find out pretty soon."

Suddenly a mysterious sound began echoing throughout the library. It was a sound that neither Twilight, Spike, nor Luna had heard before.

"What is the name of Celestia is that?" Spike asked. Just then, something large and blue materialized above Luna's head and flew across the room. It smashed into a nearby bookcase, sending pieces of paper and shards of wood flying all over the place.

"Oh no! My library!" Twilight cried. There wasn't much damage but, to Twilight, even if one book was destroyed then it was a horrible thing. Twilight, Spike, and Luna cautiously approached the mysterious object.

It was a blue box made of wood, it had windows on its sides, and it had the words _Police Public Call Box_ printed at the top.

"What is it?" Spike asked.

"I have no idea. I've never seen something like this before," Luna breathed.

"I think I have," said Twilight.

"You have?" Spike asked.

"I can't be sure but I'm think I've heard stories of mysterious blue boxes in old pony tales."

"Interesting," said Luna. The front door of the box suddenly swung open and a cloud of golden gas flew out of the opening. The gas evaporated into thin air after being in the open for a few seconds. "Curious."

Out of the box stumbled a male earth pony with a chestnut coat, dark brown mane, hourglass cutie mark, a brown suit, a light-blue undershirt, and a blue tie. He stumbled forward and fell onto the ground in front of them.

"Are you alright?" Twilight asked as she bent down to help the stallion. He looked up at Twilight as a cloud of golden gas flew out of his mouth. It wrapped around Twilight's head and then evaporated into the air. Twilight shook her head and looked the stallion straight in the eye. "I'm going to ask you again. Are you alright?"

The stallion cocked his head as he looked up at Twilight. He then gave a few weak chuckles as smaller clouds of gas flew out of his mouth.

"What's this? A talking equine of some sort? That was some ride!" he exclaimed. He then lost consciousness in Twilight's arms. The door to the stallion's strange blue box then shut by itself and locked. Twilight, Spike, and Luna exchanged confused glances as another cloud of golden gas escaped from the stallion's mouth.


	3. Twilight's Patient

Chapter 2: Twilight's Patient

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

The mysterious stallion had been lying, unconscious, in Twilight's guest bed for a whole day now. Twilight had been forced to take the following day off from work in order to take care of the mysterious pony. Luna had sent a note to Princess Celestia telling her that she'd be staying in Ponyville until the Summer Sun Celebration. Spike insisted once that they should take the stallion to a doctor but Luna refused because he was mysterious and she wanted answers from him. Twilight agreed with the Princess and was also dying of curiosity.

It was now the early evening of the day following the stallion's arrival in Ponyville. There was a knock on the door and Spike answered it. Luna was quick to enter the house and shut the door.

"Anything new?" she called upwards.

"No, Luna. Nothing!" replied Twilight from upstairs. Spike led Luna upstairs to the room where Twilight was keeping the stallion. He was still fast asleep and was showing no signs of waking up. "Every now and again that mysterious golden gas comes out of his mouth but, other than that, nothing else happens. He just sleeps."

"Have you tried to collect and study the gas?"

"Numerous times. It evaporates too quickly for me to contain it in something."

"What about the box? Have you tried opening it?"

"Yes!" Spike groaned. "We've used many different methods, both physical and magical, but that box just won't open. I assume there's an incredibly powerful curse on it."

"Enough with the curses, Spike!" Twilight snapped. Spike backed down and stepped back a couple feet.

"Oh...I'm sorry, Spike. I'm just really anxious. All of this couldn't have happened at a worse time! I mean there's only two days left until the Summer Sun Celebration and I'm stuck in my house playing nurse to a strange stallion who crashed a blue box into my bookcase!"

"I can understand your frustration," said Luna as she put a hoof on Twilight's shoulder.

"Thank you, Luna."

Luna looked over towards the stallion's bedside table and noticed a metallic, cylindrical device with a lightbulb-like tip.

"What is that?" she asked.

"No idea. We found it in one of his coat pockets," Spike replied.

"I wonder what it does."

Luna levitated the device with her horn and pointed it at a nearby chest. She noticed a button on the device and used her magic to click it. The device emanated a strange sound and the chest opened up.

"So...it unlocks stuff?" Spike asked.

"This is not like any type of magic that I've seen before," said Luna as she put the device down on the stallion's bedside table.

"I don't believe it's magical at all," said Twilight.

"What do you mean?"

"I believe it's a technological device, and a very advanced one at that."

"Maybe he knows something about your letter from the future!" Spike guessed.

"We'll find out shortly," said Twilight. Spike and Luna fell silent as Twilight proceeded to continue her examination of the stallion. Several minutes passed until she gave a long sigh and stepped back from the bed. "He's definitely not waking up anytime soon. Maybe you were right, Spike."

"Told you I was right! Wait...what was I right about?" he asked.

"I think you were right when you said we should have taken him to a doctor."

Just then, the stallion sat up and expelled a massive cloud of golden gas from his mouth which then proceeded to fly out a nearby open window.

"Did someone call me?" he asked as Twilight, Spike, and Luna jumped with surprise.

_**Carriage Road, Outskirts of Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

The air was calm and still as an earth pony named Oak Ridges walked down the deserted path. He could just make out the outlines of the buildings of Ponyville off in the distance. His orange coat and dark black hair made him stick out of the empty green scenery like a dragon in a chicken coop. He was busy tugging a wagon full of bottles of his special cow milk. He visited Ponyville once a month to restock the milk inventory of the town. He could tell that summer was definitely on the way for the sun cast its heat down on him without any type of mercy. He groaned as he stumped his front right hoof on the tip of a jagged rock.

"Ugh!" he complained. "Stupid path. Those Ponyville folk really need to make this a more comfortable road."

He shook he head and wiped the sweat from his forehead. After a long breath he continued his trek down the long path.

He began to complain about the path again when he noticed something strange. Something on the side of the road caught Oak Ridges's eye and he stopped to examine it. It was a patch of air that looked and acted like the surface of a pond. The air rippled and folded across itself as if it were alive. Oak put his hoof up to the patch of air and felt something that resembled that of liquid rubber. The rippling air then unzipped like a jacket and a hole full of blinding light appeared. Oak covered his eyes as a strange creature crawled out from the hole. Once the creature had fully squeezed its way through the hole, the air patch disappeared with the hole.

The creature that stood before Oak was something that he had never seen before. It was a strange metallic being with a dome-like top, an eye that extended like a telescope, several metallic circles on its body, and a suction cup and a strange rod, resembling a stretched egg beater, sticking out from its front chest.

"What in the name of Celestia?" breathed the surprised Oak. The creature turned towards Oak and approached him, moving along the ground as if it had wheels for feet.

"WHAT IS MY CURRENT DESTINATION?!" asked the creature with a loud, metallic voice. "EXPLAIN! EXPLAIN!"

"You're...you're...you're in Equestria."

"EQUESTRIA?! I HAVE NEVER HEARD OF SUCH A PLANET!"

"Oh...it's not a planet. It's a country...though a very large country. Our planet is named Gaia."

"GAIA?! THERE IS NO SUCH PLANET!"

"But...but there is. You're...standing on it."

The creature turned around in a circle and pointed it's telescopic eye up to the sky. Oak felt incredibly uncomfortable around the creature and desperately wanted to walk past it and just complete his job.

"Well...if you don't mind, sir, I'm just going to head off on my way," he choked. The creature seemed to ignore Oak and Oak took it as a silent goodbye. He prepared to continue walking to Ponyville when a strange cloud of golden gas flew towards them. Oak noticed that it came from the direction of Ponyville and he wondered what it was. The creature caught sight of the dust and watched as it disappeared into thin air. Oak shrugged his shoulders and prepared to leave but the creature got in his way.

"WHAT?! WHAT?! THE DOCTOR?! THE DOCTOR IS HERE?!" it screamed.

"Well...there is a doctor in Ponyville," Oak choked.

"WHERE IS THIS PONYVILLE?!"

"It's that town just over there."

"THE DOCTOR IS THERE?!"

"Well there's _a_ doctor. I think his name is Ginger Coat."

"NO! NO! THE DOCTOR'S HERE! YOU KNOW WHERE HE IS! TELL ME! TELL ME!"

"The only doctors I know are Ginger Coat and my own just a few miles back. She's named Amber Cross."

"NO! NO! NO! NO! THE DOCTOR! THE DOCTOR! GIVE ME THE DOCTOR!"

"I don't know anypony by the name of _the_ Doctor."

"LIAR! LIAR! YOU WILL TELL ME! YOU WILL TELL ME!"

"I don't know who or what you're looking for and, if you don't mind, I'll just be on my way!"

Oak turned away from the creature and began to walk away when it aimed the metal rod on its chest at him. Before Oak could react, a beam of green light shot out of the rod and hit Oak. He screamed in agony and then dropped to the ground, dead. The creature turned way from Oak's body and looked at the outline of Ponyville in the distance.

"EXTERMINATE! EXTERMINATE!" cried the creature as it started rolling its way towards the unsuspecting town.

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Twilight, Spike, and Luna couldn't take their eyes off the suddenly awakened stallion. He cocked his head a bit and chuckled.

"Strange. I seem to have ended up in a world home to anthropomorphic equines. Extraordinary!" the stallion exclaimed. He then proceeded to examine his body and began to laugh gleefully at the sight of it. "Oh my! I've regenerated into a horse myself! Incredible! Life's just full of surprises!" He then looked towards a nearby mirror and examined his mane. "Blast! Still not ginger! Who knew I'd become a horse before I became a ginger? Well dark brown seems to suit me just fine so I can live with that for now." He then examined Twilight, Spike, and Luna more closely and laughed in an even happier tone. "There are dragons in this world too? And these equines have horns and wings! Pegasi and unicorns! The humans _were_ on to something after all! Marvelous! Truly marvelous!"

"You know, we can hear every word that you're saying," said a slightly annoyed Spike.

"What? Oh yes. I've forgotten my manners. Waking up after a good regeneration can do that to someone. I'm the Doctor."

"Doctor? Doctor...who?" asked Twilight.

"Doctor nothing. I'm just the Doctor."

"Okay...well my name is Twilight Sparkle. This is my assistant and close friend, Spike, and this is the co-ruler of our land, Princess Luna."

"It is a pleasure to meet you, Doctor," said Luna.

"The pleasure is mine also," said the Doctor. "So...do you co-rule this land of...what's the name of this land?"

"Equestria."

"Ah. Interesting name. Anyway, do you co-rule this land of Equestria with your mother, the Queen?"

"No. It's just my older sister, Princess Celestia, and I."

"So do you and your sister have a mother and/or father ruling this land from far away or-"

"Like I said, it's just Celestia and I."

"Then shouldn't that make you queens?"

"Excuse me?"

"Well it only makes sense for your proper names to be _Queen_ Celestia and _Queen_ Luna since there is nobody ruling over you."

"Nopony," Twilight corrected.

"I beg your pardon?"

"You said no_body_. The correct term is no_pony_."

"Nopony?"

The Doctor then fell back on his pillow and gave out a hearty laugh.

"Nopony she says! That's what you've got to say around here?! That's brilliantly different! I'll have to get used to this!" he exclaimed joyfully. "So, what, do you say _anypony_ and _everypony_ also?"

"Actually yes," Twilight replied. The Doctor laughed again before sitting back up.

"I apologize for that sudden outburst. I'm sure I just offended you in some way. I tend to do that often."

"That doesn't surprise me," groaned Spike.

"Anyway, the correct titles for you and your sister should be Queen Celestia and Queen Luna."

"Excuse me, but we have been known as Princess Celestia and Princess Luna since the beginning of our reign and we will not change it just because a strange earth pony thinks _that's not the correct title_," snapped Luna.

"Okay. Whatever you say, _Princess Luna_."

"Cut the garbage, Doctor," said Twilight.

"Hmm?"

"I've been taking care of you for well over a day and I want some answers! Just who in Celestia's name are you?!"

"Oh so there's no belief of God in this world."

"What?"

"Oh nothing to worry your minds over."

"I'll ask you again. Who are you?"

"I told you who I am. I'm the Doctor."

"I'm pretty sure that's not your real name."

"Trust me, Tiffany. That's the name I've used for many many years. Well I've also used John Smith but that's another story."

"Tiffany? My name's Twilight. Twilight Sparkle."

"But you look so much like a Tiffany. Okay I won't call you that. What about Lavender?"

"No."

"Thalia?"

"No."

"Hermione?"

"No."

"What about Susan? You definitely look like a Susan."

"NO! My name's Twilight Sparkle and I will go by no name other than that!"

"Not even Twilight Flopple?" Spike teased. Twilight glared at the little dragon and he proceeded to back off nervously.

"Okay. Twilight it is. I'd still prefer Susan though," said the Doctor.

"We'll ask you again!" snapped Luna as she towered over the Doctor. "Who are you? What are your origins? Where are you from? What's that mysterious blue box downstairs?"

"Blue box? It's called the TARDIS."

"TARDIS?" Spike asked.

"Yes. TARDIS. Time and Relative Dimension in Space. It's my ship."

"Your...ship?"

"Yes."

"Can you show us the inside of your...uh...ship?" Twilight asked. The Doctor was about to respond when a low grumble emanated from his belly.

"I'm sorry but I'm terribly famished and in need of a warm muffin with butter. Maybe several," he chuckled. "Is there a place where I can get a good muffin?"

"Well there's Sugar Cube Corner," said Spike.

"Sugar Cube Corner? The mere name of that place gives me a cavity! Sounds good. Here's the deal. You take me to this Sugar Cube Corner for some muffins and I'll tell you everything about my origins and show you the inside of my TARDIS. Do we have a deal, Twilight Sparkle?"

Twilight rolled her eyes and groaned.

"Deal," she moaned.

"Excellent! Off to Sugar Cube Corner! I actually feel some of my masculinity slip away every time I say that name!"

The Doctor hopped out of bed and happily trotted out of the room and down the stairs.

"You know, I have to agree with him on this one. I could use a muffin myself," said Spike as he followed the Doctor downstairs. Twilight and Luna looked at each other and then followed the Doctor and the dragon out of the room, down the stairs, and out the door.


	4. A Dalek in Sugar Cube Corner

Chapter 3: A Dalek in Sugar Cube Corner

_**Sugar Cube Corner, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

The Doctor's eyes stared hungrily at the plate of warm blueberry muffins that was placed before him.

"Will that be all?" asked Mrs. Cake.

"Oh, definitely," said the Doctor as he attempted to pick up a nearby butter knife with his hoof. "Oh...blast! How do you pick things up with these confounded hooves?"

"Here," said a slightly embarrassed Twilight. "Let me help you."

She then proceeded to levitate the knife and cut the muffins open.

"Could you be so kind and spread the butter too? I'm new with all this hoof business."

Twilight rolled her eyes and spread the butter. The Doctor nodded silently as a sign of thanks and then proceeded to dive into the muffins. Mrs. Cake walked over to Twilight and whispered into her ear.

"Who is that? He sure is a strange character," she whispered.

"Even we don't know who he really is," replied Twilight. Mrs. Cake nodded goodbye to Twilight and Spike, bowed politely to Luna, and trotted back to the kitchen.

"Can I have one?" Spike asked as he turned towards the Doctor. The Doctor looked at the dragon and nodded his head. Spike took one half of a buttered muffin and began munching on it.

"My, you sure do have quite an appetite there, Doctor," Luna chuckled. The Doctor raised his head and wiped the muffin crumbs and butter from his muzzle.

"I don't know why but I suddenly have an incredibly large need for food. Must be the new body. Regenerations are always tricky to get past. The after effects can be horribly annoying," he replied.

"Excuse me, but I really don't understand."

"Understand? Oh...you must mean my talk about regenerations and such."

"Not only that, but also your lack of knowledge for the most basic of pony movements and other things that should be common sense to you."

"Well I think we've established by this point that I'm not exactly from around here."

"Then what country are you from?" Twilight asked.

"What's the name of your planet?"

"Pardon me?"

"Your planet. What's its name?"

"Uh...Gaia."

"Gaia? There's no planet named Gaia. I should know because I've had enough time to examine the stars. Unless...no. It's not possible. The barriers are sealed tight. Then again, that would explain a lot."

"What are you mumbling about?" asked an annoyed Luna.

"Huh? Oh, sorry. I tend to do that often."

"You sure do have a lot of bad habits."

"I'm just adjusting to the new body."

"You keep talking as if you've only recently become a pony," Twilight stated.

"Well that's because I _have_ only recently become a pony. Before my regeneration I resembled that of a human being."

"What's a human being?"

"No knowledge of humans? Is it possible? Have I really managed to break through the barriers?"

"Will you stop that?"

"Sorry."

"I've read through countless books and I've not once come across a creature called a human being."

"That's because they don't exist on this planet...and, now that I think about it, I doubt that they even exist in this universe at all."

Spike leaned in towards Twilight and whispered, "I don't think his mind's in the same universe as us!"

Twilight chuckled and casually pushed the dragon away from her. The Doctor was about to take another bite out of a muffin when he noticed something behind Twilight and Luna. It was a gray, female pegasus pony with somewhat strewn blonde hair and a pair of yellow eyes that seemed to be staring straight at the Doctor.

"Can I help you?" he asked politely. Twilight and Luna turned back to look at the gray pegasus. She shook her head and hiccuped in the process. "What's your name?" The pegasus turned away from the group and trotted away. "Did I say something wrong?"

"No. That's just Derpy Hooves," Spike sighed.

"Derpy Hooves? That's a cruel name."

"That's what everypony knows her as."

"Was it just me or was there something wrong with her eyes?"

"Yeah. For some reason her eyes trail off at random points. It's really weird!"

"Spike!" Twilight snapped. "She can't control it! And, besides, I don't even think Derpy Hooves is her real name. That's just what everypony knows her as."

"You don't see her complaining about it or correcting anypony. Who knows if she has another name? If she does it's probably worse than Derpy Hooves if she keeps it a secret."

"Okay! Enough talk about Derpy Hooves! We're here to talk about you, Doctor!"

"And so we are!" said the Doctor.

"So...where are you from exactly?" Luna asked.

"I'm sure that by this point you three have figured out that I'm not from your planet."

"So you're an alien?" asked a skeptical Twilight.

"Well...yes but here I'm more than an alien. You see, I'm not only from another planet...I'm from another dimension altogether!"

Twilight and Luna gave skeptical looks but Spike gave an expression that made him look as if he somewhat believed the Doctor's claims.

"That's the story you're sticking with? That you're from another dimension?" asked Twilight.

"It's the truth. I can prove it to you once I show you the inside of my TARDIS," said the Doctor with a smirk.

"Fine! Then let's go right now!"

"Fine then!"

_**Outside Town Hall, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

"Be careful up there! We don't need another hole in the roof!" called the Mayor from the ground. Rainbow Dash and another pegasus pony named Cloud Kicker were carefully moving a new piece of roof to fix up a hole in the roof of Town Hall.

"Almost there!" breathed Rainbow Dash as they lowered the piece of roof in place. It locked into place and both pegasi wiped their foreheads with relief. They flew back to the ground to meet with the Mayor. "Looks like it's a job well done!"

"Thank you! Let's hope an accident like this doesn't happen for a while! I've got to go and talk with Vinyl about her randomly turning up the volume of that stereo. I also better go check on Deep Blue and make sure that she's making a speedy recovery. See you girls later!"

The Mayor then trotted away and Cloud Kicker bid farewell to Rainbow Dash. It was just as Cloud Kicker flew away that Rainbow Dash noticed Derpy Hooves walking awkwardly, with her head down.

"Hey Derpy!" called Rainbow Dash. The cyan pegasus flew over to Derpy and landed in front of her. "What's wrong?"

"Huh? Oh...hi Rainbow Dash," Derpy breathed.

"You okay?"

"I'm fine. Might need to have a muffin later."

"Ha! You and those muffins! I prefer cupcakes myself but whatever. Listen, have you seen Twilight anywhere? I want to ask her if the library's gotten the newest Daring Doo book in yet."

"Twilight? Yeah, I just saw her in Sugar Cube Corner. She's at a table with Spike, Princess Luna, and some other pony."

"Some other pony? Who?"

"I don't know. He's new in town. He likes muffins too."

"Good for him then. Anyway, I'll see ya around!"

Rainbow was about to take off when the sounds of screaming ponies began echoing throughout the town. Rainbow and Derpy turned to see a group of ponies running away from a strange metallic creature.

"GIVE ME THE DOCTOR! GIVE ME THE DOCTOR! EXTERMINATE! EXTERMINATE!" yelled the creature.

"I'll take care of this!" stated Rainbow. She was about to fly at the creature when the creature aimed its metal rod at a nearby pony. The pony dodged the beam but a plant behind it instantly withered and died. "Strike that!"

"Maybe Twilight will know what to do!" Derpy suggested. "She got rid of that Ursa Minor so maybe she can handle this too!"

Rainbow grabbed Derpy and they flew as fast as they could towards Sugar Cube Corner.

_**Sugar Cube Corner, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

The Doctor, Twilight, Spike, and Luna had just risen from their seats when the sounds of the screaming ponies reached the shop.

"What's going on out there?" Twilight asked.

"Maybe it's a party!" cried Pinkie Pie from behind the counter. She then crossed her two front hooves and pouted. "Well why didn't they invite me?"

"I don't think it's a party, Pinkie," Spike choked. Just then, Rainbow and Derpy burst through the front door. They were both breathing heavily.

"Twilight!" cried Rainbow.

"What is it?" Twilight asked.

"Something's attacking Ponyville!"

"What? What's attacking us?"

Rainbow and Derpy turned towards each other and then turned back to Twilight.

"We...don't know what it is," Derpy replied.

Everypony turned their heads towards the door as a metallic voice cried out, "EXTERMINATE! EXTERMINATE!"

"No," breathed the Doctor as he backed up.

"What's wrong?" Luna asked.

"It's followed me! It's followed me here!"

"Do you have something to do with this?" Twilight snapped.

"I...well...yes...but it was unintentional."

Rainbow flew towards the Doctor and began to stare him down.

"And just who the hay are you, anyway?" she asked angrily.

"I'm the Doctor and right now I'm the only one who can save you all!"

"What is it? What's out there?" cried Spike. The Doctor turned towards Spike and their eyes met.

"A Dalek."

The door to Sugar Cube Corner burst open and in rolled the Dalek. Its telescopic eye scanned the room until it saw the Doctor.

"DOCTOR! IT'S THE DOCTOR! EXTERMINATE!" it cried. It aimed its death ray towards them.

"Get down!" yelled the Doctor. Everypony got down as the Dalek began firing several death beams throughout the interior of the shop. The Doctor and Twilight dived under a table and the Doctor began rummaging through his suit pockets. "Where is it? Where is it?"

"Where's what?" Twilight asked anxiously.

"My Sonic Screwdriver!"

"Your what?"

"It's a small, metal, cylindrical device with a little blue light bulb at the tip."

"I know what you're talking about."

"So you've seen it? Do you have it with you?"

"No...it's back in the guest room at the library."

"Damn! Well I think it'd be best if I got the Dalek away from everyone else."

"Everypony."

"Whatever! It's after me so it's only going to follow me. I'm going to distract it. You get every_pony_ else out of here!"

"But...Doctor-"

"You've been trying to listen and understand me since we met, Twilight Sparkle! Listen to me now and get everypony the hell out of here!"

The Doctor then jumped up and began trotting throughout the shop.

"Oi! Look at me! Look at me! I'm a target! Look at me!" he cried gleefully.

"EXTERMINATE! EXTERMINATE!" yelled the Dalek. The Dalek proceeded to focus and chase after the Doctor as Twilight managed to get everypony out through the back of the shop. The Doctor then ran towards the front door.

"Come on! Is that the best you've got? Come here! Look at me! I'm a target begging to get hit!" he laughed. The Dalek continued to yell as it shot more death beams at the prancing earth pony. He jumped out of the way and ran through the front door. The Dalek chased after him. Twilight was about to go out the back when she looked out the front window and saw the Doctor being chased.

"Twilight! Come on!" Spike called. Twilight turned back to Spike and slowly shook her head. "Where are you going?"

"I'm sorry, Spike. For some reason...I just can't leave him to handle that thing on his own. Even if he is a complete and total nutcase," Twilight breathed.

"Twilight!"

"I promise I'll come back! Don't I always keep my promises?"

Twilight ran towards the dragon and kissed him softly on the forehead. She then turned around and followed the Doctor and the Dalek out the front door.


	5. Inside the TARDIS

Chapter 4: Inside the TARDIS

_**Town Square, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Ponies continued to panic and run for their lives as the Dalek chased the Doctor through the center of town. The Dalek shot several death beams through the air and the Doctor managed to dodge each one successfully. By some stroke of luck, none of the beams hit any of the other ponies.

"That's right!" said the Doctor. "Just keep your eye on me! Focus on me and nopony else! Hey I remembered the proper term this time!"

"EXTERMINATE! EXTERMINATE!" cried the Dalek. The Doctor dodged another beam and continue on his way towards the library. He needed to get his Sonic Screwdriver and lure the Dalek into the TARDIS. There was only one way to defeat a metallic death machine of evil. The Dalek was not giving up as it continued to race after the Doctor. The Doctor smiled to himself as he managed to lure the creature back to the library. He ran for the door and...it was locked.

"Damn! Why are the doors always locked?" the Doctor snapped. The Dalek was close behind him now.

"EXTERMINATE! EXTERMINATE THE DOCTOR!" it cried. The Doctor pounded his hooves on the door but it still refused to open.

"Why did I forget my Sonic Screwdriver?"

"EXTERMINATE!"

"Damn! Damn! I have the strength of a horse and I still can't open a blasted wooden door!"

"DOCTOR! DOCTOR! EXTERMINATE!"

"I wish Donna were still here!"

"EXTERMINATE!"

Just as the Dalek was preparing to aim its death ray, somepony opened the door to the library and pulled the Doctor inside.

_**Outside Sugar Cube Corner, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Twilight ran out the front door and looked around frantically. The Doctor and the Dalek had already vanished from sight but she could still here the creature shouting for the extermination of the mysterious pony. Why was she helping him again? Why couldn't she have just joined her friends and gotten to safety? There was something about him. Something about that strange and insane Doctor that just urged Twilight to help him.

"Wait a minute...the door to the library's locked!" she exclaimed. "He'll be doomed if I'm not there in time to let him in!" She began to run quickly but she soon skidded to a halt. "Wait a minute! I can teleport! Why am I wasting time running?"

The lavender unicorn implanted an image of the inside of the library in her mind. She concentrated and closed her eyes as her horn began to glow. Then, in a flash of light, she was gone.

_**Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Twilight stumbled around for a few seconds as she teleported into the library. There was loud knocking on the door and she could hear the Dalek outside.

"DOCTOR! DOCTOR! EXTERMINATE!" cried the Dalek.

"I wish Donna were still here!" exclaimed the Doctor.

"EXTERMINATE!"

Twilight ran over to the door, unlocked it, opened it, and pulled the Doctor inside. The Doctor stumbled back as Twilight closed and locked the door.

"What? How did you get here?" he asked.

"Teleportation," replied Twilight with a snarky tone. "Duh."

"Teleportation! Ingenious! I should have known that you could perform magic, I mean with you being a unicorn and all."

"EXTERMINATE!" cried the Dalek from outside.

"Right! Dalek first. Amazement later."

Twilight nodded and they ran upstairs as fast as they could.

The Doctor burst into the guest room and quickly found his Sonic Screwdriver.

"Aha! There you are!" he exclaimed.

"So are you going to kill it with that?" Twilight asked.

"What? Kill a Dalek with _this_? Please!"

"Then why did you race here to get it?"

"I couldn't just leave my Sonic Screwdriver behind! Besides, I have a plan that will rid us of our little metallic menace!"

"Okay. What's your plan then?"

"We need to lure it into the TARDIS."

"So we're going to trap it in there?"

"No! We're going to kill it in there. We'll be in there too."

Twilight stared at the Doctor in disbelief.

"We're going to be in that tiny box with that fat...thing?" she asked.

"Just wait until you see the inside! Ah! We best not keep our guest waiting!"

The Doctor ran downstairs and Twilight was quick to follow. The door burst open and the Dalek was now inside.

"EXTERMINATE!" it cried.

"Yes. Exterminate and all that. But first, you'll have to get my friend Twilight and I out of my humble abode!" teased the Doctor. The Doctor grabbed Twilight and pulled her towards the blue box. He raised his right hoof and then sighed. "I forgot. No fingers."

He then rose his other hoof and clapped them together. The doors of the TARDIS opened wide and the Doctor pushed her in.

"Are you sure about this, Doctor?" asked a frightened Twilight.

"Positive!" answered the Doctor as he pushed her through the doors. Once inside, the Doctor was quick to close and lock the doors. Twilight shook her head and soon gained a grasp of her surroundings. They were now in a massive room with a giant control center in the middle of it. There were several openings to hallways that seemed to go on for miles.

"Where...where are we?" asked a stunned Twilight.

"Twilight Sparkle of Equestria, I introduce you to the inside of the TARDIS!" announced the Doctor as he ran towards the control center.

"It's bigger on the inside-"

"Than it is on the outside. Geez! Maybe you ponies aren't so different from humans after all."

The doors leading into the TARDIS began to shake and Twilight stepped back.

"Can it get in?" she asked nervously.

"Why yes it can," replied the Doctor. "I believe we have around...less than a minute before it gets in."

"Then what?"

"Then we take care of it."

"How? Do you have a...Dalek-killing machine or something?"

"No. I just have a brilliantly simple plan!"

"EXTERMINATE! EXTERMINATE!" cried the Dalek.

"He should be getting in right about...now!"

The doors to the TARDIS burst open and in rolled the Dalek. It continued to scream and blast death rays as it entered.

"Come on, Ms. Sparkle! Follow me!" said the Doctor as he grabbed the confused unicorn by the tail.

"Doctor!" yelled Twilight as she followed the Doctor down one of the hallways. Twilight turned back to see the Dalek rolling after them quickly."If we get killed then I'm so going to make you pay for it!"

"And I'd deserve every bit of it. Now just shut up and follow me!"

Twilight fell silent as she continued to follow the Doctor through a series of turns and doorways. Eventually they came to a large silver door that made the Doctor beam with excitement. The ponies ran through the door and found themselves standing next to a massive indoor swimming pool.

"What else do you have in this thing?" asked a now amazed Twilight. "A forest?"

"I've been thinking about that to be honest. Now stand right here on the edge of the pool and I'll be back in a jiffy!" said the Doctor. Twilight stood at the edge of the pool as the Doctor disappeared through another doorway. Twilight took deep breaths as the screams of the Dalek drew closer and closer. Everything seemed to slow down. All she could think about was the promise she made to Spike.

"I promise I'll come back!" she had said. "Don't I always keep my promises?"

Twilight gulped and remembered the fear and confusion that had been etched onto Spike's face. She couldn't die and let him down. The pain of losing her would kill him. She wouldn't die. The Doctor would protect her. Or would he? What if he had left there as bait while he made a clean getaway? Twilight jumped as the doors flew open.

"DOCTOR! DOCTOR! WHERE IS THE DOCTOR?" screamed the Dalek.

"I...I don't know," lied Twilight.

"NO! NO! YOU KNOW! YOU WERE WITH THE DOCTOR! TELL ME WHERE HE IS OR I SHALL KILL YOU!"

"I...don't know where he is."

"LIAR! LIAR! YOU KNOW WHERE HE IS! TELL ME!"

"I don't know where he is!"

"TELL ME! I SHALL EXTERMINATE HIM!"

The Dalek aimed its death ray at Twilight and she backed up. She suddenly heard a strange sound and looked up.

"You're right, Dalek. I do know where the Doctor is," she said with a smile.

"WHERE IS HE THEN?" asked the Dalek.

"Up."

"WHAT?"

There was a loud clanging sound as the Doctor landed on top of the Dalek. Twilight jumped out of the way and the Doctor managed to break off the Dalek's telescopic eye.

"NO! NO! MUST EXTERMINATE THE DOCTOR! MUST EXTERMINATE THE DOCTOR! MUST NOT LOSE!" it screamed. The Dalek spun madly out of control and moved closer and closer towards the pool.

"Sorry my unwanted guest. You've just lost the game!" said the Doctor with a chuckle. He then jumped off of the Dalek, pushing the creature back with his hind legs in the process. The Dalek toppled over into the pool. Sparks of electricity covered the metallic body of the Dalek as it screamed in agony. Soon the screaming stopped and the fizzing metal body sank towards the bottom of the pool. "Well that was easy!"

"Water? That's its weakness?" Twilight asked.

"Too much of it. There is electricity and a living creature in that suit after all. Just add water and...we both know what happens then."

"What _did_ you do to that thing to make it want to kill you?"

"I destroyed its entire species."

"Oh."

"And yet they still seem to keep making unwanted comebacks. Oh well. Well my work here's done. Let's get you back to your friends!"

"Thank you, Doctor."

The Doctor and Twilight walked calmly down the hallway. They were almost back to the control room when the entire ship shook violently.

"What was that?" Twilight asked.

"Oh no," breathed the Doctor. He broke into a run and Twilight followed. They returned to the control room to find the large control panel heavily damaged. "Damn it! That Dalek must have hit it with one of its rays!"

The open doors to the TARDIS shut on their own and the ship began to vibrate. The Doctor ran up to the control panel and began moving and tinkering with several different buttons and levers.

"Doctor...what's happening?" Twilight asked. The Doctor looked up at Twilight and sighed.

"It's too late. The TARDIS is damaged...and we're leaving," he replied.

"Leaving? I can't leave! Where's it taking us?"

"The question isn't only where it's taking us. The question is also _when_ it's taking us."

The TARDIS gave a massive jolt and the sound that Twilight heard earlier began echoing throughout the ship.

"No! I can't leave! I can't go! I promised Spike I'd come back! Take me back! Doctor! Take me back!"

"Hold on, Twilight!"

The TARDIS gave another massive jolt and they were gone. Flying through the ribbons of existence to an unknown time, place, or both.

_**Outside the Home of Twilight Sparkle, Ponyville, Equestria, Gaia, Spring, 1002 C.E.**_

Derpy had seen the whole thing. She had seen the Dalek follow the Doctor and Twilight into the library. Things had grown oddly quiet now. Maybe she should go get help. But then maybe it would be too late by the time she got back! She had to check things out. Make sure everything was okay. Derpy slowly trotted over towards the library.

She peeked inside with caution and entered quietly.

"Hello? Twilight? Uh...what was his name again? Oh yeah! Doctor? Are any of you in here?" she asked. There was no response. She looked around the library and saw that there were many scorch marks on the walls and on the books. It was then that her eyes fell onto the mysterious blue box. "Police Public Call Box. Wonder what that means." She approached the box and noticed that the doors were open. She only managed to get a peak inside when the doors suddenly shut. "What?" The light on the top of the box began to flicker on and off and the box slowly began to disappear into thin air. "What? Where? Who? WHAT?" Within seconds the box was gone and the mysterious sound it had been emitting had vanished also. "Twilight? Doctor? Was that you who just left?"

"Yes," replied a female voice. "It was them."

Derpy turned around to see a beautiful mare with a dark red coat, dark purple mane, and sharp blue eyes standing in the doorway.

"Who...who are you?" Derpy asked.

"You'll come to know me well in good time, Derpy Hooves," replied the mare.

"How do you know my name?"

"How else would I know your name? You told it to me, silly!"

"But I've never met you before!"

"But _I've_ certainly met _you_ before."

"What do you mean by that? Have...have you been stalking me?"

"No dearie. Nothing like that. Don't worry about dear Twilight or the Doctor. You'll see them again soon. In fact, I only just got back from seeing them."

"You saw them defeat that creature?"

"No. I know how you feel, Derpy. This may all sound confusing now but, don't worry, it'll all make sense in due time."

"Who the hay are you? Answer me!"

"A friend. And that's all you need to know for now. Have a nice day Derpy Hooves and be patient! Your time for adventure is coming soon."

The mare winked at Derpy and then backed out the doorway.

"Wait!" called Derpy. She ran for the doorway but found nopony there. The air was still, the world was silent, and many questions were buzzing around Derpy Hooves's head.

To be continued...


End file.
